Description

Ribosome profiling (ribo-seq) is a technique that takes advantage of NGS
technology to sequence ribosome-protected mRNA fragments and consequently
allows the locations of translating ribosomes to be determined at the entire
transcriptome level (Ingolia et al., 2009).

For a more detailed description of the protocol, see Ingolia et al.
(2012). For reviews on this technique and its applications, please refer to
Ingolia (2014) and Michel et al. (2013).

This track displays cumulative ribo-seq data obtained from human cells under
different conditions and can be used for the exploration of human genomic loci
that are being translated. The values on the y-axis represent the number of
ribosome footprint sequence reads at a given position. As of February
2016, the track contains data from 9 studies (see References section for
details). Further details about the aggregated track and additional ribo-seq
data from these and other studies including data obtained from other organisms
can be found at the specialized ribo-seq browser
GWIPS-viz.

Methods

For each study used to generate this track, raw fastq files were downloaded from
a repository (e.g., NCBI GEO datasets).
Cutadapt
was used to trim the relevant adapter sequence from the reads, after which reads
below 25 nt in length were discarded. The trimmed reads were aligned to
ribosomal RNA using
Bowtie
and aligning reads were discarded. The remaining reads were then aligned to the
hg38 (GRCh38) genome assembly using Bowtie. An offset of 15 nt (to infer the
position of the A-site) was added to the most 5' nucleotide coordinate of each
uniquely-mapped read.

The alignment files from each of the included studies were merged to generate
this aggregate track.

See individual studies at
GWIPS-viz for a full
description of the methods of data acquisition and processing.

Credits

Thanks to Audrey Michel, Stephen Kiniry and GWIPS-viz for providing the data for
this track. If you wish to cite this track, please reference: